rs1555865385
Positions:
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PM4_SupportingPP5
The NM_152296.5(ATP1A3):c.410_412delCCT(p.Ser137del) variant causes a disruptive inframe deletion change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: not found (cov: 31)
Consequence
ATP1A3
NM_152296.5 disruptive_inframe_deletion
NM_152296.5 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.97
Genes affected
ATP1A3 (HGNC:801): (ATPase Na+/K+ transporting subunit alpha 3) The protein encoded by this gene belongs to the family of P-type cation transport ATPases, and to the subfamily of Na+/K+ -ATPases. Na+/K+ -ATPase is an integral membrane protein responsible for establishing and maintaining the electrochemical gradients of Na and K ions across the plasma membrane. These gradients are essential for osmoregulation, for sodium-coupled transport of a variety of organic and inorganic molecules, and for electrical excitability of nerve and muscle. This enzyme is composed of two subunits, a large catalytic subunit (alpha) and a smaller glycoprotein subunit (beta). The catalytic subunit of Na+/K+ -ATPase is encoded by multiple genes. This gene encodes an alpha 3 subunit. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
PM1
In a transmembrane_region Helical (size 20) in uniprot entity AT1A3_HUMAN there are 5 pathogenic changes around while only 0 benign (100%) in NM_152296.5
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_152296.5. Strenght limited to Supporting due to length of the change: 1aa.
PP5
Variant 19-41986174-TAGG-T is Pathogenic according to our data. Variant chr19-41986174-TAGG-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 503717.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=1, Likely_pathogenic=2}.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP1A3 | NM_152296.5 | c.410_412delCCT | p.Ser137del | disruptive_inframe_deletion | 5/23 | ENST00000648268.1 | NP_689509.1 | |
ATP1A3 | NM_001256214.2 | c.449_451delCCT | p.Ser150del | disruptive_inframe_deletion | 5/23 | NP_001243143.1 | ||
ATP1A3 | NM_001256213.2 | c.443_445delCCT | p.Ser148del | disruptive_inframe_deletion | 5/23 | NP_001243142.1 | ||
ATP1A3 | XM_047438862.1 | c.320_322delCCT | p.Ser107del | disruptive_inframe_deletion | 5/23 | XP_047294818.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP1A3 | ENST00000648268.1 | c.410_412delCCT | p.Ser137del | disruptive_inframe_deletion | 5/23 | NM_152296.5 | ENSP00000498113.1 | |||
ENSG00000285505 | ENST00000644613.1 | n.410_412delCCT | non_coding_transcript_exon_variant | 5/25 | ENSP00000494711.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:2Uncertain:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
ATP1A3-associated neurological disorder Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Molecular Genetics, Royal Melbourne Hospital | Nov 11, 2021 | This sequence change is predicted to cause a change in the length of the protein due to an in-frame deletion of one amino acid in a non-repeat region of the ATP1A3 protein (p.(Ser137del)). The region deleted is highly conserved (100 vertebrates, UCSC), and is located in a transmembrane helical region. This variant is absent from gnomAD v2.1 and v3.1. This variant has been reported in at least two probands with dystonia-parkinsonism, and has been reported to segregate with disease in eight affected family members from a single family (Royal Melbourne Hospital; PMID: 25359261, described as c.443_445delGAG, p.Ser148del). It has been classified as a variant of uncertain significance and likely pathogenic (ClinVar ID: 503717). Furthermore, two missense variants at the same position (p.Ser137Phe and p.Ser137Tyr) have been identified in cases with alternating hemiplegia of childhood (PMID: 22842232). Based on the classification scheme RMH Modified ACMG Guidelines v1.4.0, this variant is classified as LIKELY PATHOGENIC. Following criteria are met: PP1_Strong, PS4_Supporting, PM2_Supporting, PM4_Supporting. - |
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Jan 25, 2018 | The c.410_412delCCT variant in the ATP1A3 gene has been reported previously to segregate in a family with dystonia, with one unaffected family member also reported to harbor the c.410_412delCCT variant suggesting reduced penetrance for this variant (Wilcox et al., 2014). This variant causes an in-frame deletion of codon Serine 137, denoted p.Ser137del. The c.410_412delCCT variant is not observed in large population cohorts (Lek et al., 2016). In-silico analyses, including protein predictors and evolutionary conservation, support a deleterious effect. We interpret c.410_412delCCT as a likely pathogenic variant. - |
Dystonia 12 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 09, 2017 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the deleted amino acid is currently unknown. This variant has been reported to segregate with disease in a single family affected with dystonia (PMID: 25359261). This variant is also referred to as c.443_445del (p.Ser148del) in the literature. This variant is not present in population databases (ExAC no frequency). This variant, c.410_412delCCT, results in the deletion of 1 amino acid(s) of the ATP1A3 protein (p.Ser137del), but otherwise preserves the integrity of the reading frame. - |
Computational scores
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at